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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagtaattttgtgagtcatgtacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagccctccacaa...

Basic information

species Glycine max
transcript GLYMA17G13040.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G13040.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G704032_T03 (Zea mays), 5'ss of exon 12
GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagt---aattttgtgagtc--atg-tacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagccctccacaa
|||||||| || ||||||||| | || |||||| ||||||| || ||||  | | ||||||| |||||||| ||||||||||||   | | |  |  | | ||  |    ||||| | | |   ||| || | |     |||  | |  | |       | || || || |   ||    ||     
GTTTGGAGGCTACAGGCAGCTTTGGGAGAACAATCTGAAATCACCAAGTGTACCAAACAGGAATATGAAAGGCTTCAAAATgtagccccctttgctgtgactgcattcttattttttcatttgaatgatattcacttcatatgccctttacacaaaagga-atcatttaggtccaacttgtc-----

upper sequence: GLYMA17G13040.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G18470.1 (Arabidopsis thaliana), 5'ss of exon 12
GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagtaattttgtgagtcatgtacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagccctccacaa---
|| |||||||| || ||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||||     | |      |||| |  |||||| | |    |  ||    | ||  | ||||    |||     ||  ||| | ||   | | || ||     
GTGTGGAGACTTCAAGCAGCACTTGGTGAACAAACAGAAATCACAAAATTCAGCCAGCAGGAATATGAAAGACTGCAAAATgtatattcatttattagccatga-tgtttttgtaactttcttgtttcgattttactttttcc---ctttgcttaatcctgtgtcaatgtgtcttctactccag

upper sequence: GLYMA17G13040.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G18470.2 (Arabidopsis thaliana), 5'ss of exon 11
-------------------GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagtaattttgtgagtcatgtacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagccctccacaa---
                   || |||||||| || ||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||||     | |      |||| |  |||||| | |    |  ||    | ||  | ||||    |||     ||  ||| | ||   | | || ||     
TCTAATTTGATATCTCTAGGTGTGGAGACTTCAAGCAGCACTTGGTGAACAAACAGAAATCACAAAATTCAGCCAGCAGGAATATGAAAGACTGCAAAATgtatattcatttattagccatga-tgtttttgtaactttcttgtttcgattttactttttcc---ctttgcttaatcctgtgtcaatgtgtcttctactccag

upper sequence: GLYMA17G13040.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv17s0000g04160.t01 (Vitis vinifera), 5'ss of exon 12
GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagtaattttgtgagtcatgtacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagcc--ctccacaa-
|| |||||||| || || || ||||| || ||| | ||||| ||||||| |||  | ||||||||||||||||||||||||||| |   |  |||||| | |||   ||| |     ||||  |  | ||  ||  || |   ||  |    | | | |||| |  | ||||   ||| |||| 
GTGTGGAGACTTCAAGCTGCACTTGGTGAGCAATCAGAAATCACAAAGTACAGTAAGCAGGAGTATGAAAGACTTCAAAATgtaaatttctcaaccttgactgatcgattctt---atcatagatatgtgacgtgcatgtctgaacttggtgactttcatgttttgacaagctatctcaacaac

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|51341177|gb|CO982494.1|CO982494
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|11413717|gb|BF425728.1|BF425728
EST:     AAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|4296915|gb|AI442543.1|AI442543
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|19346249|gb|BM891129.1|BM891129
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|13479627|gb|BG508970.1|BG508970
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|11414150|gb|BF426161.1|BF426161
EST:     AAACTGAAATTACAAAGATCAGCCTACATGAGTATGAAAGACTTCAAAAT                         GAGACAGTGTTATGCAGAGTTTGGTTCGAGGGAGAGATTAACGTT
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTT
EST: gi|8403908|gb|BE059542.1|BE059542
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
EST: gi|13791494|gb|BG654085.1|BG654085
EST:     AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAAT                         GAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG
genomic: AAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacaca ... gtggtatcagGAGAAAGTGTTATGCAGAGTTTGTTTCGAGGGAGAGATTAACGTTGTACTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGGAGACTCCAGGCAGCTCTTGGCGAACAAACTGAAATTACAAAGTTCAGCCAACAGGAGTATGAAAGACTTCAAAATgtataacacataaccttaaatgagtaattttgtgagtcatgtacttatgctgtatatcttccaaagtttctaatatgatgtatgaagaagccctccacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccac